Sample 3300001433

Basic Information
IMG/M Taxon OID	3300001433 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0090294 \| Gp0057739 \| Ga0012500
Sample Name	Switchgrass rhizosphere bulk soil microbial communities from Kellogg Biological Station, Michigan, USA, with PhiX - S5
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Basic Information

IMG/M Taxon OID

3300001433 Open in IMG/M

GOLD Reference
(Study | Sequencing Project | Analysis Project)

Gs0090294 | Gp0057739 | Ga0012500

Sample Name

Switchgrass rhizosphere bulk soil microbial communities from Kellogg Biological Station, Michigan, USA, with PhiX - S5

Sequencing Status

Permanent Draft

Sequencing Center

DOE Joint Genome Institute (JGI)

Published?

Use Policy

Open

Dataset Contents
Total Genome Size	12795419
Sequencing Scaffolds	22
Novel Protein Genes	23
Associated Families	23

Dataset Contents

Total Genome Size

12795419

Sequencing Scaffolds

Novel Protein Genes

Associated Families

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae	1
All Organisms → cellular organisms → Bacteria	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	4
Not Available	9
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	2
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	1

Dataset Phylogeny

Taxonomy Groups

Number of Scaffolds

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae

All Organisms → cellular organisms → Bacteria

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria

Not Available

All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium

All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales

Ecosystem Assignment (GOLD)
Name	Corn, Switchgrass And Miscanthus Rhizosphere Microbial Communities From Kellogg Biological Station, Michigan, Usa
Type	Environmental
Taxonomy	Environmental → Terrestrial → Soil → Unclassified → Grasslands → Corn, Switchgrass And Miscanthus Rhizosphere → Corn, Switchgrass And Miscanthus Rhizosphere Microbial Communities From Kellogg Biological Station, Michigan, Usa

Ecosystem Assignment (GOLD)

Name

Corn, Switchgrass And Miscanthus Rhizosphere Microbial Communities From Kellogg Biological Station, Michigan, Usa

Type

Environmental

Taxonomy

Environmental → Terrestrial → Soil → Unclassified → Grasslands → Corn, Switchgrass And Miscanthus Rhizosphere → Corn, Switchgrass And Miscanthus Rhizosphere Microbial Communities From Kellogg Biological Station, Michigan, Usa

Alternative Ecosystem Assignments
Environment Ontology (ENVO)	terrestrial biome → rhizosphere → bulk soil
Earth Microbiome Project Ontology (EMPO)	Host-associated → Plant → Plant rhizosphere

Alternative Ecosystem Assignments

Environment Ontology (ENVO)

terrestrial biome → rhizosphere → bulk soil

Earth Microbiome Project Ontology (EMPO)

Host-associated → Plant → Plant rhizosphere

Location Information
Location	Kellogg Biological Station, Michigan, USA
Coordinates	Lat. (^o)	42.3948	Long. (^o)	-85.3738	Alt. (m)	N/A	Depth (m)	0
Location on Map

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Location Information

Location

Kellogg Biological Station, Michigan, USA

Coordinates

Lat. (^o)

42.3948

Long. (^o)

-85.3738

Alt. (m)

N/A

Depth (m)

Location on Map

Zoom:

Family	Category	Number of Sequences	3D Structure?
F001244	Metagenome / Metatranscriptome	738	Y
F002508	Metagenome / Metatranscriptome	553	Y
F016084	Metagenome / Metatranscriptome	250	Y
F019338	Metagenome / Metatranscriptome	230	Y
F020927	Metagenome / Metatranscriptome	221	N
F025757	Metagenome	200	N
F029148	Metagenome	189	Y
F038467	Metagenome / Metatranscriptome	166	N
F039759	Metagenome	163	Y
F039800	Metagenome / Metatranscriptome	163	Y
F041906	Metagenome / Metatranscriptome	159	Y
F049092	Metagenome	147	N
F049708	Metagenome / Metatranscriptome	146	Y
F054114	Metagenome	140	Y
F057488	Metagenome	136	N
F063850	Metagenome	129	N
F063987	Metagenome / Metatranscriptome	129	N
F065229	Metagenome / Metatranscriptome	128	Y
F083399	Metagenome	113	N
F088958	Metagenome	109	Y
F089000	Metagenome	109	N
F101715	Metagenome / Metatranscriptome	102	Y
F102094	Metagenome / Metatranscriptome	102	Y

Family

Scaffold	Taxonomy	Length	IMG/M Link
JGI24036J14985_100079	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae	3686	Open in IMG/M
JGI24036J14985_100164	All Organisms → cellular organisms → Bacteria	2998	Open in IMG/M
JGI24036J14985_100235	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	2641	Open in IMG/M
JGI24036J14985_100238	Not Available	2633	Open in IMG/M
JGI24036J14985_100810	Not Available	1444	Open in IMG/M
JGI24036J14985_100848	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1398	Open in IMG/M
JGI24036J14985_100918	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1336	Open in IMG/M
JGI24036J14985_100929	Not Available	1329	Open in IMG/M
JGI24036J14985_100947	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1307	Open in IMG/M
JGI24036J14985_101250	Not Available	1108	Open in IMG/M
JGI24036J14985_101445	Not Available	1017	Open in IMG/M
JGI24036J14985_101683	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	907	Open in IMG/M
JGI24036J14985_101734	Not Available	887	Open in IMG/M
JGI24036J14985_102129	Not Available	771	Open in IMG/M
JGI24036J14985_102643	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia	660	Open in IMG/M
JGI24036J14985_102653	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	658	Open in IMG/M
JGI24036J14985_102837	All Organisms → cellular organisms → Bacteria	632	Open in IMG/M
JGI24036J14985_103251	All Organisms → cellular organisms → Bacteria	579	Open in IMG/M
JGI24036J14985_103403	Not Available	564	Open in IMG/M
JGI24036J14985_103427	Not Available	562	Open in IMG/M
JGI24036J14985_103510	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	553	Open in IMG/M
JGI24036J14985_103546	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia	549	Open in IMG/M

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI24036J14985_100079	JGI24036J14985_1000791	F029148	GWKDIEIKYRGKPVKGRYNVSDNLVTVVAWSGTKTARLGVLPAERLAKMLLRELADQGETK*
JGI24036J14985_100164	JGI24036J14985_1001641	F057488	ATAQLAVGPVPIMSSINGIPITVSVTSWITVNSVGDETTVDARIFADLIDLQKKFSDVVDSFKRSARNCNRSADGQNPVVSFKSGSLWPRNDQLIMFVRGDIDIWSCSVGPPQSAIRWEKTKVSFLTLKLPVRRTWRNVKRNMDGTQPFHGTLLVSLAEKDGANVALRNTEPNLRLDGEPTFATNANLSLAKTDMNDKVSKTLRSAIDLTKLKDVLPKELQKFNMTVNSARFRDRGGHAIAEINLVGKASSTTTTSLLQQIDAGL*
JGI24036J14985_100235	JGI24036J14985_1002355	F065229	MLLIRFAISGFALMLLGLAVSLSVAQSEDETNAAQAATFIHQ*
JGI24036J14985_100238	JGI24036J14985_1002386	F049092	MKFIEPAFDTGGDLWRPPLNVPDSDAHALNEKFARQSAELRLRLTEVLELHNVQQRQANELQDRYDDIDRLSQTVSALQEAVNQYKMGTAAAEDKIILLESEKAVLQAQLD
JGI24036J14985_100810	JGI24036J14985_1008101	F063850	MRLVVVIGVVALVALPEIANAASVQDVFQEFGLFGTWATDCNSPATPGNPYVNITAPSAGLVLEDHDLGPDFAVNRYSVLSAEPVSQTSVSVQVIFQPGTTVEERQKLVFSVNNNTRRTIFNQS
JGI24036J14985_100848	JGI24036J14985_1008481	F019338	GSHYGFDADRQWRPIFRLGVLGSMPAMRRTEAVLTAGAVACLAFVSIVYPVFAQDVDPRCKDIFDKVACTCAVRNGGHVIPPPVGVKREGLKLRPKEEAGGTQTLDGGRVAFPKYYRREGLKFHRSRALEGYLACMRAAGRK*
JGI24036J14985_100918	JGI24036J14985_1009181	F083399	MAEESAVSGDTRSWGFFATFVLGAIAFLAGQLAGMAALVGWYGFDLRNVPVLSQHGGAIIVFIFVSAPVQVAILALAAGYKGNIADYLGYKLPRRGEVVLCLAILAAMIAVGDAMSWLAGRSVVDRFQTDIYQAANSVGQLPLL
JGI24036J14985_100929	JGI24036J14985_1009294	F089000	MGEPTPATPASKYFAATVAMIAGAFFFAVGAGLLPIPGGPSNLHGPLWLLLCVGLAFFLAGLAILIPMLGHANDSGDLPAGAPFWLRAMQYLIGLCIFACF
JGI24036J14985_100947	JGI24036J14985_1009473	F049708	QIMSRGWRAWSRTGWGTVMRVKWVLIGFGILYLVFALSFIPTDKILPRPIEESWELVRDILWAGMTIISIGLLEVMSPLATPFASASGLRRGDVAEILLAVILVAAAVYSALRLRRKDLTPRWRGTHTFFLLLALTLVAIVRFTLYSWSHFA*
JGI24036J14985_101250	JGI24036J14985_1012501	F039759	AAWVASGGRVPQGAYGRRPTPLEPLRPSRLLDTFLPGHRSQDVTLWEGAVFALSSLLFVAASMAPFYGIRRVQNAFQSTFATQVQQVCPAQPPEAMIACWAQFYPWSRVAIDLGAPIVIAVICLVLANRLRHFGRQHFINRLAELKVLPAASTLFLRAFRDDQVRIRRASRNLFSSVFDLGRVPATLDELMLERLDGRGDLIAIGNPQDRKGAARQSPWGAQRLYVDDAHWQETVTMLARDADRIVLCIDASDGVRWEIAHVLQSGHAGKTLFFLNPSTDVQTRKRQLQEDFGVSAADLASIDVDRVLALRTTSTDQLILMVCDKPERDAYLVAARLAFEGRAGNLTMSAKGR*
JGI24036J14985_101445	JGI24036J14985_1014451	F038467	RIGDWILRPHFSEQKDKKQKEKRLDRCTAQLTNADKITMIYSLDTHYMWTLELSNPSWNFPSGSKFDVSFGNRERGYFRQRVAALDPQLVRVLLPDSLNSFEAFRRLFKLDVVAGGLTTQFDLAYANQVLLALTQCVTKFGMTTKSKAAITAYLKSPIGPAAEANSDPAIVQEAFSLAGAIVAEGEIAKAAALKPDEIPDGVSGDTVWKVADNLFTISVLPKDAVPAEIGDLNDLIVGGNAQKCRGDFFAGAMLDVVESTTIARAYTTCQTQQAATSTYYFAMPRKQGGGLYLTKIIATGVEVPPTIERAIKELDAKVRGVITAALARL*
JGI24036J14985_101683	JGI24036J14985_1016832	F088958	RNCFISLVFCAWRNSAREFQGHGCKWPTPRSNAGSFAPRLDTKLTNFGKLSSNGPCLPFGYQMKWPMPSDAKSSPWFHEVRPEIVPPHSFCQTLFPTFKASLFESAKACAISGQTAISAVAITANGKPPPQNRWHSCFLDVRHLSISVRLSAATNLKLERRGNTIL*
JGI24036J14985_101734	JGI24036J14985_1017342	F101715	MRDFGEYLRAYWAYVLANLGWGKALSVALVWLAGMFAPLVAKTLLELPNWMAMTWMIVWAVLGYIF
JGI24036J14985_102129	JGI24036J14985_1021291	F025757	HPPFKAIESKARLKAWSFATRAPMSYSTSISLFWLEMAVLIGCVVLSIRMRSRAAMWVALAIVAHCAVWLAIHDEEILIRLVASALVYLGLLKFSPNAARVWLCAGGALAGAFLLGTMALSLLMSFPGRWSVFGLSMGATLLFLTSGLLIGFWVVYRWTDPTQLGDTQPRQEA*
JGI24036J14985_102643	JGI24036J14985_1026431	F063987	MKFVSLTKSTAVPHQILGTSTNEKRELLMCGHSLIARLTIAIFLFQTPGVTSGVHAEKPDSTVETSSVGKRKLVIGPSSTSVALGKASLIVSPLTHRDGSYVGDYQLKVK
JGI24036J14985_102653	JGI24036J14985_1026531	F002508	MPMSNDDDTHVYTRWRDSQVSRNFHRLGLLVAAIILIAGLLLMAKDALGVRFWDLIPADIPILAGGIAIGLTGIGLVSLAAYGIVRAVGWAID
JGI24036J14985_102837	JGI24036J14985_1028371	F001244	PTGAAEVAQRLAAFPFTPPDVKLKEKEPLSSSNDWFTKHDKKKIDELGSLDFYASSGAQSVGVVPKLHNTSAGIEIYQLPPXLTKETFEKTEGPYRSGVTKKYSNKRSGXKIAKFKAGTMAQSGLACFHMSRLLGHLVEVPPATYRTMDLQEFQKVGDQARTTGHPSCTEAWAQLRAIAKSGSSKLILPDGKTVYGSLAQNPRGEDSSPE
JGI24036J14985_103145	JGI24036J14985_1031451	F102094	MYVLIVVIGVLSQGASVVPVGVTSQIVGKFKNLDECKAAAKQPHAAGPIADITVV
JGI24036J14985_103251	JGI24036J14985_1032511	F016084	MLEPSADEIREWENAVTQFMIEYLGGLRDRPVYRHTTSHEIRSGLDPKLPTKGTDF
JGI24036J14985_103403	JGI24036J14985_1034031	F020927	MWAAFVRQFAAYAITRRGKKLFALIGVLALCFGAALLIDMQFYVSASFAALLAGFAAVTYVVQHVKLKRAEHQRLLRKAEAA
JGI24036J14985_103427	JGI24036J14985_1034271	F054114	AYSMDERKKPVPAYTIEPMKRKTVVNRTVKDEIGFRIVPTDVEVEGYMVRTLRGDSVFLSHEDVVRLKLDRNLVPMLIEGGDDTPVGMQQMNAALSDKQKTALDVLTRLVESDPSLVEKLLASKEPEQVEE*
JGI24036J14985_103510	JGI24036J14985_1035101	F041906	MKKKSTSQSAFFNLRVLIAAVFCLAGVAVGLLAMGAVSSVFAQAKAAKTNQDAPGTQTPDVVRMVGPVSLNQDLRTLPYVAPKKKFEERGPLTRYPHLHTDQTSAPSGYGTAGLPNVQNLLKNVWRPAPTIPSPLLTFEGYGDCCANIVPDNMGD
JGI24036J14985_103546	JGI24036J14985_1035462	F039800	MSAADATRSKGVASFRTRLFTAIMIIVATLTALGFYLAQRR

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300001433: Switchgrass rhizosphere bulk soil microbial communities from Kellogg Biological Station, Michigan, USA, with PhiX - S5

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences